CHEM 351 : Chemicals Big and Small: Nano-material to Bio-macromolecules


2024 Semester One (1243) (15 POINTS)

Course Prescription

Chemical materials are found with a broad range of shapes, sizes and physical properties. Students will study the synthesis of chemical materials; including polymeric materials using radical chemistry, inorganic materials and proteins and peptides using synthetic and biological chemical approaches. Methods to characterise materials will be investigated, including a range of physical and computational techniques giving insight into molecular interactions.

Course Overview

Block 1: Introduction to nanomaterials and Biomolecules (Carbohydrates, Peptides and Proteins)
Block 2: Physical and Computational Chemistry: An introduction to current methods in computational chemistry and molecular modeling
Block 3: Polymer Chemistry and Kinetics: Polymeric materials, synthesis techniques (esp. the free radical chemistry and its use for free radical polymerization), polymerization kinetics, polymer characterization, and applications.
Block 4: Biological Chemistry;  Recombinant Protein Production; Chemistry and Synthesis of Nucleic Acids; Serine Protease and Glycosidase: Mechanism and Kinetics; Target Identification; Emerging Topics in Chemical Biology.

Course Requirements

Prerequisite: 30 points from CHEM 251, 252, 253 Restriction: CHEM 350

Capabilities Developed in this Course

Capability 2: Sustainability
Capability 3: Knowledge and Practice
Capability 4: Critical Thinking
Capability 5: Solution Seeking
Capability 6: Communication
Capability 7: Collaboration
Capability 8: Ethics and Professionalism
Graduate Profile: Bachelor of Science

Learning Outcomes

By the end of this course, students will be able to:
  1. Apply computational modelling for molecules and reactions using various specialized software packages (Capability 3, 4 and 5)
  2. Describe various methods to synthesise and characterise polymers and outline the various applications of polymeric materials (Capability 3, 4 and 5)
  3. Use and apply the principles of radical reactions and describe various radical reactions in organic and polymer synthesis and biological systems (Capability 3, 4 and 5)
  4. Describe and discuss various methods for the synthesis, analysis and modification of carbohydrates, peptides/proteins and biomolecules, including those featuring metals (Capability 3, 4 and 5)
  5. Communicate results of laboratory and computational analysis in various ways including in forms for a non-technical audience. (Capability 2, 3, 4, 5, 6, 7 and 8)


Assessment Type Percentage Classification
Test 15% Individual Coursework
Laboratories 25% Individual Coursework
Assignments 10% Individual Coursework
Quizzes 5% Individual Coursework
Tutorials 5% Individual Coursework
Final Exam 40% Individual Examination
Assessment Type Learning Outcome Addressed
1 2 3 4 5
Final Exam

A student must pass both the theory component and the practical component to gain an overall pass. The theory component is composed of quizzes, term tests, and final exams. The practical component is composed of laboratory experiments.


Tuākana Science is a multi-faceted programme for Māori and Pacific students providing topic specific tutorials, one-on-one sessions, test and exam preparation and more. Explore your options at

As part of the University-wide Tuākana community, The School of chemical sciences aims to provide a welcoming learning environment for and enhance the success of, all of our Māori and Pacific students. We are led by the principles of tautoko (support) and whanaungatanga (connection) and hope you find a home here at the School. Students who have identified as Māori and/or Pacific will receive an invitation to our online portal introducing the Programme, the resources we have available, and how you can get involved.

Tuākana Chemistry runs a range of activities for students enrolled in this class. This includes weekly workshops, social activities, and opportunities to engage with senior students and researchers within the School of Chemical Sciences. Tuākana-eligible students will be added automatically to the Tuākana Chemistry program when they enroll in this course. For more information, please see the Tuākana program website or email

Key Topics

Topic 1: An introduction to current methods in computational chemistry and molecular modelling

• Background on theoretical and computational methods used in chemistry.
• Capabilities, limitations, and reliability of various computer-based methods such as force field, first-principles calculation, and machine learning
•  Concepts of potential energy surface, optimization, transition state searches, and molecular dynamics (linking to topics 3 and 4)
• Choosing proper computational tools for different applications.
• Application of computation chemistry in different areas of chemistry including heterogeneous catalysis, material chemistry, surface chemistry, biological chemistry, and drug discovery (link to topic 4) 

Topic 2: Polymer Chemistry and Kinetics 

Linear polymers and network polymers, examples of synthetic and naturally occurring biopolymers (links to topics 1 and 4)
• Polymer nomenclature, polymer size, understanding polymer conformation (links to topic 2)
• Uncontrolled polymerization methods, in particular free-radical polymerization (FRP). Understanding factors influencing the polymerization kinetics of FRP and calculation of rate constant, conversion (links to lab experiment)
•  Principles of GPC and their use in determining molecular weight in polymers and molecular weight distribution. (links to lab experiment)
•  Concept of polymer gels, comparing natural vs man-made gelling polymers (links to topic 4). Synthesis of polymer gel, characterization, and applications
• Controlled radical polymerization chemistry and compare it to conventional uncontrolled free radical polymerization to make polymers, photopolymerization, radical polymerization kinetics, chain transfer and termination processes, degree of polymerization control, and RAFT polymerization techniques.

Topic 3:  Nanomaterials, Molecular Self-Assembly and Biomolecules

• Introduction to various classes of ‘larger’ molecules, highlighting nanomaterials, polymers, and biomolecules are much ‘larger’ than classes of molecules taught in previous courses.
• Overview of nanostructures and nanomaterials, nomenclature, classification, natural and artificial nanomaterials, Differences between nanomaterials and bulk materials
• Properties: particle size, surface area, quantum effects,
• Examples of nanomaterials: micelles, synthetic polymers, large biomolecules (links to topics 2 and 4): carbon nanotubes,   control of nano architecture, Synthesis – top-down and bottom-up methods, molecular self-assembly
• Self-assembled peptide nanomaterials (links to lab experiment)
• Potential toxicity and environmental impact from nanoparticles
• Biomolecules: Carbohydrates, Amino Acids, Peptides, and Proteins, Molecular Self-Assembly

Topic 4: Biological Chemistry

This topic assumes on a strong understanding of stage 2 organic chemistry, and a high school level understanding of biology.

• Classes of biomolecules including proteins, carbohydrates, and nucleic acids. Understanding the organization of these biomolecules from small monomeric units to larger macromolecules (links to topic 2).
• The process of turning biomolecular monomers into biopolymers; from amino acids to proteins, simple to complex carbohydrates and nucleotides into nucleic acids.
• The flow of information in biological systems according to the central dogma, and the chemical basis of the transfer of this information
• Organisation of proteins starting from amino acid building blocks, the structure of α-amino acids, and their zwitterionic nature, isoelectric points, and understanding the importance of amino acid side chains in the formation of peptide secondary structures and protein folding. Primary, secondary, tertiary, and quaternary structures in proteins. posttranslational modifications, and interactions of proteins with small molecules.
• Synthetic organic chemistry techniques for polymeric biomolecules including proteins, carbohydrates, and nucleic acids including basics of polysaccharide synthesis, amino acid synthesis, solid phase peptide and nucleic acid synthesis (links to lab experiment).
• Understand various examples of self-assembly in biomolecules (links to topic 3)
• Characterization and visualisation methods for nucleic acids and proteins, including their 3D structure, through experimental and computational methods.
• Biological production and purification methods for biomolecules.
• DNA and protein sequencing and structure determination including amino acid analysis, peptide sequencing reactions
• Understand enzymes, enzyme mechanisms, and enzyme kinetics (links to lab experiment).

Special Requirements

Attendance at the laboratories is a compulsory part of this course. Students must be wearing safety glasses, covered footwear, and a lab coat before entering the laboratory and must keep these on until after exiting the laboratory. Jandals or other open shoes are not satisfactory footwear. Students who wear prescription spectacles are required to wear safety glasses over their spectacles. Students must comply with all health and safety regulations whilst working in the laboratories.

Workload Expectations

This course is a standard 15-point course and students are expected to spend 10 hours per week involved in each 15-point course that they are enrolled in.

For this course, you can expect 32 hours of lectures, 20 hours of reading and thinking about the content, and 37 hours of work on assignments and/or test preparation.

Delivery Mode

Campus Experience

Campus Experience

Attendance is required at scheduled activities including labs/tutorials to receive credit for components of the course.

Lectures will be available as recordings. Other learning activities will not be available as recordings.

The course will not include live online events.

Attendance on campus is required for the test and exam.

The activities for the course are scheduled as a standard weekly timetable.

Learning Resources

Course materials are made available in a learning and collaboration tool called Canvas which also includes reading lists and lecture recordings (where available).

Please remember that the recording of any class on a personal device requires the permission of the instructor.

All course material will be available on Canvas. This includes lecture recording links and videos of laboratory techniques.

Student Feedback

During the course Class Representatives in each class can take feedback to the staff responsible for the course and staff-student consultative committees.

At the end of the course students will be invited to give feedback on the course and teaching through a tool called SET or Qualtrics. The lecturers and course co-ordinators will consider all feedback.

Your feedback helps to improve the course and its delivery for all students.

Course content has been fine tuned  based on student feedback

Academic Integrity

The University of Auckland will not tolerate cheating, or assisting others to cheat, and views cheating in coursework as a serious academic offence. The work that a student submits for grading must be the student's own work, reflecting their learning. Where work from other sources is used, it must be properly acknowledged and referenced. This requirement also applies to sources on the internet. A student's assessed work may be reviewed for potential plagiarism or other forms of academic misconduct, using computerised detection mechanisms.

Class Representatives

Class representatives are students tasked with representing student issues to departments, faculties, and the wider university. If you have a complaint about this course, please contact your class rep who will know how to raise it in the right channels. See your departmental noticeboard for contact details for your class reps.


The content and delivery of content in this course are protected by copyright. Material belonging to others may have been used in this course and copied by and solely for the educational purposes of the University under license.

You may copy the course content for the purposes of private study or research, but you may not upload onto any third party site, make a further copy or sell, alter or further reproduce or distribute any part of the course content to another person.

Inclusive Learning

All students are asked to discuss any impairment related requirements privately, face to face and/or in written form with the course coordinator, lecturer or tutor.

Student Disability Services also provides support for students with a wide range of impairments, both visible and invisible, to succeed and excel at the University. For more information and contact details, please visit the Student Disability Services’ website

Special Circumstances

If your ability to complete assessed coursework is affected by illness or other personal circumstances outside of your control, contact a member of teaching staff as soon as possible before the assessment is due.

If your personal circumstances significantly affect your performance, or preparation, for an exam or eligible written test, refer to the University’s aegrotat or compassionate consideration page

This should be done as soon as possible and no later than seven days after the affected test or exam date.

Learning Continuity

In the event of an unexpected disruption, we undertake to maintain the continuity and standard of teaching and learning in all your courses throughout the year. If there are unexpected disruptions the University has contingency plans to ensure that access to your course continues and course assessment continues to meet the principles of the University’s assessment policy. Some adjustments may need to be made in emergencies. You will be kept fully informed by your course co-ordinator/director, and if disruption occurs you should refer to the university website for information about how to proceed.

The delivery mode may change depending on COVID restrictions. Any changes will be communicated through Canvas.

Student Charter and Responsibilities

The Student Charter assumes and acknowledges that students are active participants in the learning process and that they have responsibilities to the institution and the international community of scholars. The University expects that students will act at all times in a way that demonstrates respect for the rights of other students and staff so that the learning environment is both safe and productive. For further information visit Student Charter


Elements of this outline may be subject to change. The latest information about the course will be available for enrolled students in Canvas.

In this course students may be asked to submit coursework assessments digitally. The University reserves the right to conduct scheduled tests and examinations for this course online or through the use of computers or other electronic devices. Where tests or examinations are conducted online remote invigilation arrangements may be used. In exceptional circumstances changes to elements of this course may be necessary at short notice. Students enrolled in this course will be informed of any such changes and the reasons for them, as soon as possible, through Canvas.

Published on 31/10/2023 10:51 a.m.